There is no restriction on what one uses to set up individual parameter getter/setters, though there are some other options implemented in BioPerl (for instance, Bio::Root::RootI::_set_from_args()).

A key requirement is there be a way to detect changes in the state of the ParameterBaseI object so that any object with a Bio::ParameterBaseI can decide whether to submit a new request or return cached data. State changes are revealed by the returned values of the parameters_changed() method, which is a simple boolean set to TRUE when the object is first instantiated or parameters have changed.

When retrieving anything using the implementation-specific to_* methods (such as to_query, to_string, to_uri, to_request, etc), the ParameterBaseI object state is set to FALSE to indicate the data has been accessed and indicate reaccessing will retrieve the same value. The observing object can then independently decide whether to rerun the cached query or return a previously cached result.

One can also use indiviual getter/setters to retrieve single parameter values as well as use parameter_hash() to retrieve all of the parameters in one go as a hash. To check which parameters are available use available_parameters(). Args passed to

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@lists.open-bio.org - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.

https://github.com/bioperl/bioperl-live/issues

AUTHOR

Email cjfields at bioperl dot org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _